The rockefeller university

BACKGROUND: Alefacept treatment is highly effective in a select group patients with moderate-to-severe psoriasis, and is an ideal candidate to develop systems to predict who will respond to therapy. A clinical trial of 22 patients with moderate to severe psoriasis treated with alefacept was conducted in 2002-2003, as a mechanism of action study. Patients were classified as responders or non-responders to alefacept based on histological criteria. Results of the original mechanism of action study have been published. Peripheral blood was collected at the start of this clinical trial, and a prior analysis demonstrated that gene expression in PBMCs differed between responders and non-responders, however, the analysis performed could not be used to predict response. METHODS: Microarray data from PBMCs of 16 of these patients was analyzed to generate a treatment response classifier. We used a discriminant analysis method that performs sample classification from gene expression data, via "nearest shrunken centroid method". Centroids are the average gene expression for each gene in each class divided by the within-class standard deviation for that gene. RESULTS: A disease response classifier using 23 genes was created to accurately predict response to alefacept (12.3% error rate). While the genes in this classifier should be considered as a group, some of the individual genes are of great interest, for example, cAMP response element modulator (CREM), v-MAF avian musculoaponeurotic fibrosarcoma oncogene family (MAFF), chloride intracellular channel protein 1 (CLIC1, also called NCC27), NLR family, pyrin domain-containing 1 (NLRP1), and CCL5 (chemokine, cc motif, ligand 5, also called regulated upon activation, normally T expressed, and presumably secreted/RANTES). CONCLUSIONS: Although this study is small, and based on analysis of existing microarray data, we demonstrate that a treatment response classifier for alefacept can be created using gene expression of PBMCs in psoriasis. This preliminary study may provide a useful tool to predict response of psoriatic patients to alefacept.

Glutamate is the major fast excitatory amino acid transmitter in the CNS, and exerts its action through receptors that function as ion channels such as NMDA receptors (NMDARs), AMPA receptors (AMPARs), and kainate receptors (KARs), and also through signaling cascades via metabotropic receptors. Of the ionotropic receptors, NMDARs and AMPARs have been extensively studied for decades, while relatively fewer studies have focused on the role of the KARs in the glutamatergic synapse. Despite this, there is considerable experimental data that suggest a major role for KARs in modulating synaptic transmission and plasticity, particularly in the hippocampal formation, as well as an involvement in disease states. KARs mediate most aspects of kainate-induced seizures and excitotoxic cell death, and thus, are a rational drug target for antiepileptic drug discovery. Recent data from human studies have also highlighted a role for KARs in certain psychiatric diseases, such as schizophrenia and major depression, and a recent association of KAR gene variants with response to antidepressants has brought considerable interest in developing a clearer understanding of KAR action in the brain. We have recently found that exposure to stress and stress hormone administration can produce contrasting changes in KAR subunit expression in the rat hippocampus, suggesting that a modification of hippocampal KARs by stress may be a mechanism for predisposing individuals to stress-related psychiatric diseases. Here, we review the anatomical and functional characteristics of hippocampal KARs, their role in synaptic plasticity, their regulation by certain hormones, and briefly review what is known about their involvement in disease states such as epilepsy and depression. (C) 2010 Elsevier Inc.

Objective: Based on a small sample of cases with schizophrenia and control individuals from an isolated population, a genome-wide association study was undertaken to find variants conferring susceptibility to this disease. Methods: Standard association tests were employed, followed by newer multilocus association methods (genotype patterns). Results: Individually, no variant produced a significant result. However, the best two variants (rs1360382 on chromosome 9 and rs1303 on chromosome 14) showed significantly different genotype pattern distributions between patients and control individuals. The risk genotype pattern AA-TT is highly predictive of schizophrenia, with estimated sensitivity and specificity of 1 and 0.96, respectively. Conclusions: These findings support the hypothesis that schizophrenia is partly due to multiple genetic variants, each with a relatively small effect. Copyright (C) 2010 S. Karger AG, Basel

The display of copulatory behaviors usually requires the presence of a mate and is, therefore, preceded by a search for and approach to a potential partner. The intensity of approach behaviors is determined by a process labeled sexual incentive motivation. Although it is known that female sexual motivation depends on estrogens, their site of action within the brain is unknown. In the present experiment, we obtained data relevant to this issue. An shRNA encoded within an adeno-associated viral (AAV) vector directed against the estrogen receptor alpha (ER alpha) gene (or containing a nonsense base sequence as a control treatment) was injected bilaterally into the ventromedial nucleus of the hypothalamus (VMN) or the posterodorsal amygdala (MePDA) of female rats. After an 80% reduction of the number of ER alpha in the VMN, sexual incentive motivation was absent after treatment with estradiol and progesterone. Proceptivity and receptivity were also much reduced, while the number of rejections was enhanced. Suppression of the ER alpha in the MePDA lacked these effects. Likewise, the inactive control AAV vector failed to modify any behavior. Thus, the ER alpha in the VMN, but not in the MePDA, is important for proceptivity and receptivity as well as for sexual incentive motivation. These results show that ER alpha in the VMN is crucial for the entire sequence of behavioral events from the processes leading to the establishment of sexual contact until the accomplishment of copulatory behaviors. Copyright (C) 2009 S. Karger AG, Basel

In vivo studies suggest that replication forks are arrested due to encounters with head-on transcription complexes. Yet, the fate of the replisome and RNA polymerase (RNAP) following a head-on collision is unknown. Here, we find that the E. coli replisome stalls upon collision with a head-on transcription complex, but instead of collapsing, the replication fork remains highly stable and eventually resumes elongation after displacing the RNAP from DNA. We also find that the transcription-repair coupling factor, Mfd, promotes direct restart of the fork following the collision by facilitating displacement of the RNAP. These findings demonstrate the intrinsic stability of the replication apparatus and a novel role for the transcription-coupled repair pathway in promoting replication past a RNAP block.

We introduce a novel graph-based kernel method for annotating functional residues in protein structures. A structure is first modeled as a protein contact graph, where nodes correspond to residues and edges connect spatially neighboring residues. Each vertex in the graph is then represented as a vector of counts of labeled non-isomorphic subgraphs (graphlets), centered on the vertex of interest. A similarity measure between two vertices is expressed as the inner product of their respective count vectors and is used in a supervised learning framework to classify protein residues. We evaluated our method on two function prediction problems: identification of catalytic residues in proteins, which is a well-studied problem suitable for benchmarking, and a much less explored problem of predicting phosphorylation sites in protein structures. The performance of the graphlet kernel approach was then compared against two alternative methods, a sequence-based predictor and our implementation of the FEATURE framework. On both tasks, the graphlet kernel performed favorably; however, the margin of difference was considerably higher on the problem of phosphorylation site prediction. While there is data that phosphorylation sites are preferentially positioned in intrinsically disordered regions, we provide evidence that for the sites that are located in structured regions, neither the surface accessibility alone nor the averaged measures calculated from the residue microenvironments utilized by FEATURE were sufficient to achieve high accuracy. The key benefit of the graphlet representation is its ability to capture neighborhood similarities in protein structures via enumerating the patterns of local connectivity in the corresponding labeled graphs.

Innovations in antisense drug design have enhanced potency and selectivity, as demonstrated in a recent study by Lanford and colleagues, who treated hepatitis C virus (HCV)-infected chimpanzees with SPC3649. This compound is a second-generation antisense RNA molecule that is complementary to the microRNA miR-122, a major regulatory RNA in liver that fine-tunes the expression of over 100 cellular genes and enhances HCV replication. Serum concentrations of cholesterol and HCV RNA were reduced in chimpanzees treated with 12 weekly intravenous infusions of SPC3649, and no major side effects were noted, paving the way for clinical trials of SPC3649 and other antisense drugs directed against microRNAs. Potential therapeutic uses of SPC3649 include the treatment of HCV infection and liver cancer.

Following transcription of the SRY gene on the Y chromosome of genetic males, a cascade of genomic and biochemical events causes the developing brain to be influenced by two testosterone metabolites, the potent androgen dihydrotestosterone and the aromatization product estradiol (E2). These steroid hormones binding to their cognate nuclear receptors produce differential gene expression profiles between male and female brains, and as a result, male-typical sex behaviors appear in adulthood and female-typical sex behaviors are suppressed. Although anatomical and cellular substrates underlying sexually dimorphic brain and behavior have been identified, still very little information is available about the molecular mechanisms involved. Microarray technology is a powerful technique that can be a used to assess the changes in thousands of gene transcripts simultaneously. Thus such high-throughput screening may be a useful initial step in the identification of estrogen-responsive genes involved in the sexual differentiation of brain.

Activation of transcription in response to low oxygen tension is mediated by the hypoxia-inducible factor-1 (HIF-1). HIF-1 is a heterodimer of two proteins: aryl hydrocarbon receptor nuclear translocator and the oxygen-regulated HIF-1 alpha. The C-terminal activation domain of HIF-1 alpha has been shown to interact with cysteine/histidine-rich region 1 (CH1) of the coactivator CBP/p300 in a hypoxia-dependent manner. However, HIF forms lacking C-terminal activation domain (naturally occurring or genetically engineered) are still able to activate transcription of target genes in hypoxia. Here, we demonstrate that the N-terminal activation domain (N-TAD) of HIF-1 alpha interacts with endogenous CBP and that this interaction facilitates its transactivation function. Our results show that interaction of HIF-1 alpha N-TAD with CBP/p300 is mediated by the CH3 region of CBP known to interact with, among other factors, p53. Using fluorescence resonance energy transfer experiments, we demonstrate that N-TAD interacts with CH3 in vivo. Coimmunoprecipitation assays using endogenous proteins showed that immunoprecipitation of CBP in hypoxia results in the recovery of a larger fraction of HIF-1 alpha than of p53. Chromatin immunoprecipitation demonstrated that at 1% O(2) CBP is recruited to a HIF-1 alpha but not to a p53 target gene. Upon activation of both pathways, lower levels of chromatin-associated CBP were detected at either target gene promoter. These results identify CBP as the coactivator directly interacting with HIF-1 alpha N-TAD and mediating the transactivation function of this domain. Thus, we suggest that in hypoxia HIF-1 alpha is a major CBP-interacting transcription factor that may compete with other CBP-dependent factors, including p53, for limiting amounts of this coactivator, underscoring the complexity in the regulation of gene expression by HIF-1 alpha.